{"entity": "researcher", "timestamp": "2026-06-17T19:29:02.769Z", "family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "affiliations": ["Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e"}}, "publications": [{"entity": "publication", "iuid": "2b2c9cd55b354c8c805f7b3f3749f406", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b2c9cd55b354c8c805f7b3f3749f406.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b2c9cd55b354c8c805f7b3f3749f406"}}, "title": "Warming-Induced Effects on Microbial Communities and Nitrogen Cycling Capacity in Tundra Litter Are Modulated by Herb Abundance and Litter Quality.", "authors": [{"family": "Jeanbille", "given": "Mathilde", "initials": "M", "orcid": "0000-0002-7758-8928", "researcher": {"href": "https://publications.scilifelab.se/researcher/aec9e57ba006483381b852b505728277.json"}}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE", "orcid": "0000-0002-9627-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a4e19bdfc1431c9dd1c3f1cd58c766.json"}}, {"family": "Juhanson", "given": "Jaanis", "initials": "J", "orcid": "0000-0003-3799-2819", "researcher": {"href": "https://publications.scilifelab.se/researcher/43736fc1dba8405285b1143f5ba3f170.json"}}, {"family": "Michelsen", "given": "Anders", "initials": "A", "orcid": "0000-0002-9541-8658", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1ae80fdcd1949869986ad85c68a5586.json"}}, {"family": "Alatalo", "given": "Juha", "initials": "J", "orcid": "0000-0001-5084-850X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e31e5ef78cd941ffb26abd000ea418c1.json"}}, {"family": "Cooper", "given": "Elisabeth J", "initials": "EJ", "orcid": "0000-0002-0634-1282", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e24fe660b0540ea9b977e022b22a82d.json"}}, {"family": "Henry", "given": "Greg H R", "initials": "GHR", "orcid": "0000-0002-2606-9650", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec146a7b05534922b90d3205f12b5716.json"}}, {"family": "Hofgaard", "given": "Annika", "initials": "A", "orcid": "0000-0001-6919-5537", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cb3c8abbf684418a75b41492e83ad5c.json"}}, {"family": "Hollister", "given": "Robert D", "initials": "RD", "orcid": "0000-0002-4764-7691", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e541fcf014f49e38fccb53eeb989b64.json"}}, {"family": "J\u00f3nsd\u00f3ttir", "given": "Ingibj\u00f6rg S", "initials": "IS", "orcid": "0000-0003-3804-7077", "researcher": {"href": "https://publications.scilifelab.se/researcher/89fc1fd6b2b84dba86483c9e25d2a214.json"}}, {"family": "Klanderud", "given": "Kari", "initials": "K", "orcid": "0000-0003-1049-7025", "researcher": {"href": "https://publications.scilifelab.se/researcher/11f070d4cdfa40e3addf23592be1c840.json"}}, {"family": "Tolvanen", "given": "Anne", "initials": "A", "orcid": "0000-0002-5304-7510", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ea61db4d29d428091e2bce0ae8d00a9.json"}}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Glob Chang Biol", "issn": "1365-2486", "issn-l": "1354-1013", "volume": "31", "issue": "11", "pages": "e70582"}, "abstract": "Climate warming is changing tundra vegetation in the Arctic, with implications for plant litter properties. Warming may thus modify bacterial and fungal communities and their nitrogen (N) cycling capacity in the litter layer, which in turn can affect plant N availability. To address potential warming effects, we characterized the responses of bacterial and fungal communities and their genetically encoded capacity for inorganic N-transformations in the litter layer, as well as 15N natural abundance in the underlying soil layer as an integrated measure of N processes in the soil, in 16 long-term alpine and Arctic tundra warming experiments distributed across 12 circumpolar locations. Although abundance, diversity, and composition of microbial communities were structured by the local conditions rather than experimental warming, warming indirectly modified microbial communities and their capacity for N transformations through changes in litter quality. Specifically, experimental warming resulted in stronger connections between the capacity for nitrification, denitrification and N-fixation in the litter and the \u03b415N signature in the soil. These warming-induced connections were mainly mediated by increased dominance of herbs but also increased litter mass. These findings suggest accelerated inorganic N cycling in the litter layer with warming, particularly coupled to local abundance of herbs, which can create positive feedback on plant growth as well as ecosystem respiration. Thus, microbial communities in the litter may contribute to an intensification of ongoing vegetation shifts across the tundra biome.", "doi": "10.1111/gcb.70582", "pmid": "41221642", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "NGI Stockholm (Genomics Production)": null, "NGI Short read": null}, "xrefs": [{"db": "pmc", "key": "PMC12606403"}], "notes": [], "created": "2025-11-16T14:52:02.241Z", "modified": "2025-11-21T14:19:43.976Z"}, {"entity": "publication", "iuid": "78586428e6d44db2a96ef24198fe1489", "links": {"self": {"href": "https://publications.scilifelab.se/publication/78586428e6d44db2a96ef24198fe1489.json"}, "display": {"href": "https://publications.scilifelab.se/publication/78586428e6d44db2a96ef24198fe1489"}}, "title": "Denitrification is a community trait with partial pathways dominating across microbial genomes and biomes.", "authors": [{"family": "Pold", "given": "Grace", "initials": "G", "orcid": "0000-0002-7536-3944", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a78bb0a7f6043119b6be5e226983d04.json"}}, {"family": "Sagha\u00ef", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0002-7069-2159", "researcher": {"href": "https://publications.scilifelab.se/researcher/0341d780c3ad44e3bce819fbc38c0176.json"}}, {"family": "Jones", "given": "Christopher M", "initials": "CM"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}], "type": "journal article", "published": "2025-10-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "9495", "issn-l": "2041-1723"}, "abstract": "Diverse microorganisms can execute one or more steps in denitrification, during which nitrate or nitrite is successively reduced into nitric oxide, nitrous oxide, and ultimately dinitrogen. Many of the best-characterized denitrifiers are complete denitrifiers capable of executing all steps in the pathway, but their dominance in natural communities and what metabolic traits and environmental factors drive the global distribution of complete vs. partial denitrifiers are unclear. To address this, we conducted a comparative analysis of denitrification genes in 61,293 genomes, 3991 metagenomes, and 413 terrestrial and aquatic metatranscriptomes. We show that partial denitrifiers outnumber complete denitrifiers and the potential to initiate denitrification is more common than the potential to terminate it, particularly in nutrient rich environments. Our results further indicate that complete denitrifiers tend to be fast-growing organisms, favoring organic acid over sugar metabolism, and encoding the ability to oxidize and reduce a broader range of organic and inorganic compounds compared to partial denitrifiers. This suggests complete denitrifiers are metabolically flexible opportunists. Together, our results indicate an environmental footprint on the presence of denitrification genes which favors the genomic potential for partial over complete denitrification in most biomes and highlight that completion of the denitrification pathway is a community effort.", "doi": "10.1038/s41467-025-65319-5", "pmid": "41152293", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12569097"}, {"db": "pii", "key": "10.1038/s41467-025-65319-5"}], "notes": [], "created": "2025-11-28T10:46:06.036Z", "modified": "2025-11-28T10:46:06.107Z"}, {"entity": "publication", "iuid": "e679aca133c2422599ac1891a96c1a05", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e679aca133c2422599ac1891a96c1a05.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e679aca133c2422599ac1891a96c1a05"}}, "title": "Resistance and resilience of co-occurring nitrifying microbial guilds to drying-rewetting stress in soil", "authors": [{"family": "M\u00fcller", "given": "Laura J", "initials": "LJ", "orcid": "0009-0009-5747-2432", "researcher": {"href": "https://publications.scilifelab.se/researcher/11dad561c7e24e68b9ed71a015aa2263.json"}}, {"family": "Alicke", "given": "Mara", "initials": "M", "orcid": "0009-0000-0244-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5d4c9a20fc04322a8babeaded66302f.json"}}, {"family": "Romdhane", "given": "Sana", "initials": "S", "orcid": "0000-0003-0295-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/494ad3e37974440988db1f7b377bae76.json"}}, {"family": "Pold", "given": "Grace", "initials": "G", "orcid": "0000-0002-7536-3944", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a78bb0a7f6043119b6be5e226983d04.json"}}, {"family": "Jones", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-2723-6019", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c04ad1e78da45ee8b383fb09fc5d44a.json"}}, {"family": "Sagha\u00ef", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0002-7069-2159", "researcher": {"href": "https://publications.scilifelab.se/researcher/0341d780c3ad44e3bce819fbc38c0176.json"}}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}], "type": "journal-article", "published": "2025-09-00", "journal": {"title": "Soil Biology and Biochemistry", "issn": "0038-0717", "volume": "208", "pages": "109846", "issn-l": null}, "abstract": null, "doi": "10.1016/j.soilbio.2025.109846", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:13:11.714Z", "modified": "2025-09-08T07:13:12.028Z"}, {"entity": "publication", "iuid": "408854eb0c68488e8f43d442b1150e6c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/408854eb0c68488e8f43d442b1150e6c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/408854eb0c68488e8f43d442b1150e6c"}}, "title": "Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.", "authors": [{"family": "Siljanen", "given": "Henri M P", "initials": "HMP", "orcid": "0000-0002-3197-1438", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a1fb0f39c4547438d0cdb35457a312c.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "Hilts", "given": "Angus S", "initials": "AS"}, {"family": "Bagnoud", "given": "Alexandre", "initials": "A"}, {"family": "Alves", "given": "Ricardo J E", "initials": "RJE"}, {"family": "Jones", "given": "Christopher M", "initials": "CM"}, {"family": "Kerou", "given": "Melina", "initials": "M"}, {"family": "Sousa", "given": "Felipa L", "initials": "FL"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}, {"family": "Biasi", "given": "Christina", "initials": "C"}, {"family": "Schleper", "given": "Christa", "initials": "C", "orcid": "0000-0002-1918-2735", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ef5a3f76ba14a498f4eb6f0a7eeb465.json"}}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "5", "issue": "1", "pages": "ycaf183", "issn-l": null}, "abstract": "Microorganisms are key players in the global cycling of nitrogen and carbon, controlling their availability and fluxes, including the emissions of the powerful greenhouse gases nitrous oxide and methane. Standard sequencing methods often reveal only a limited fraction of their diversity, because of their low relative abundance, the insufficient sequencing depth of traditional metagenomes of complex communities, and limitations in coverage of DNA amplification-based assays. Here, we developed and tested a targeted metagenomics approach based on probe capture and hybridization to simultaneously characterize the diversity of multiple key metabolic genes involved in inorganic nitrogen and methane cycling. We designed comprehensive probe libraries for each of the 14 target marker genes comprising 264 111 unique probes. In validation experiments with mock communities, targeted metagenomics yielded gene profiles similar to the original communities. Only GC content had a small effect on probe efficiency, as low GC targets were less efficiently detected than those with high GC, within the mock communities. Furthermore, the relative abundances of the marker genes obtained using targeted or traditional shotgun metagenomics were significantly correlated. In addition, using archaeal amoA genes as a case-study, targeted metagenomics identified a substantially higher taxonomic diversity and a larger number of sequence reads per sample, yielding diversity estimates 28 or 1.24 times higher than shotgun metagenomics or amplicon sequencing, respectively. Our results show that targeted metagenomics complements current approaches to characterize key microbial populations and functional guilds in biogeochemical cycles in different ecosystems, enabling more detailed, simultaneous characterization of multiple functional genes.", "doi": "10.1093/ismeco/ycaf183", "pmid": "41221508", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12598625"}, {"db": "pii", "key": "ycaf183"}], "notes": [], "created": "2025-11-21T12:38:28.515Z", "modified": "2025-11-21T12:38:28.801Z"}, {"entity": "publication", "iuid": "f3a2e9a2ed934057bcdb6be6711ac846", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3a2e9a2ed934057bcdb6be6711ac846.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3a2e9a2ed934057bcdb6be6711ac846"}}, "title": "Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes.", "authors": [{"family": "Sagha\u00ef", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0002-7069-2159", "researcher": {"href": "https://publications.scilifelab.se/researcher/0341d780c3ad44e3bce819fbc38c0176.json"}}, {"family": "Pold", "given": "Grace", "initials": "G"}, {"family": "Jones", "given": "Christopher M", "initials": "CM"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}], "type": "journal article", "published": "2023-12-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "8249", "issn-l": "2041-1723"}, "abstract": "Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes (nirK, nirS) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.", "doi": "10.1038/s41467-023-44022-3", "pmid": "38086813", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10716430"}, {"db": "pii", "key": "10.1038/s41467-023-44022-3"}], "notes": [], "created": "2024-11-25T10:16:12.005Z", "modified": "2024-11-25T10:16:12.056Z"}, {"entity": "publication", "iuid": "d15cf4e4b2eb403d9ed06962d64bd8a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d15cf4e4b2eb403d9ed06962d64bd8a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d15cf4e4b2eb403d9ed06962d64bd8a6"}}, "title": "Contrasting plant-soil-microbial feedbacks stabilize vegetation types and uncouple topsoil C and N stocks across a subarctic-alpine landscape.", "authors": [{"family": "Casta\u00f1o", "given": "Carles", "initials": "C", "orcid": "0000-0002-2403-7006", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7bfa857714f425886c4484c15eb59a5.json"}}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}, {"family": "Egelkraut", "given": "Dagmar", "initials": "D", "orcid": "0000-0002-2644-2144", "researcher": {"href": "https://publications.scilifelab.se/researcher/c360cf5cb53c43e582e95487d8c0a949.json"}}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD", "orcid": "0000-0002-3384-4547", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7a40688d33545a19c3c666940bda255.json"}}, {"family": "Olofsson", "given": "Johan", "initials": "J", "orcid": "0000-0002-6943-1218", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e9ecce51d244e0ab066f315aae8548d.json"}}, {"family": "Clemmensen", "given": "Karina Engelbrecht", "initials": "KE", "orcid": "0000-0002-9627-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a4e19bdfc1431c9dd1c3f1cd58c766.json"}}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "238", "issue": "6", "pages": "2621-2633", "issn-l": "0028-646X"}, "abstract": "Global vegetation regimes vary in belowground carbon (C) and nitrogen (N) dynamics. However, disentangling large-scale climatic controls from the effects of intrinsic plant-soil-microbial feedbacks on belowground processes is challenging. In local gradients with similar pedo-climatic conditions, effects of plant-microbial feedbacks may be isolated from large-scale drivers. Across a subarctic-alpine mosaic of historic grazing fields and surrounding heath and birch forest, we evaluated whether vegetation-specific plant-microbial feedbacks involved contrasting N cycling characteristics and C and N stocks in the organic topsoil. We sequenced soil fungi, quantified functional genes within the inorganic N cycle, and measured 15 N natural abundance. In grassland soils, large N stocks and low C : N ratios associated with fungal saprotrophs, archaeal ammonia oxidizers, and bacteria capable of respiratory ammonification, indicating maintained inorganic N cycling a century after abandoned reindeer grazing. Toward forest and heath, increasing abundance of mycorrhizal fungi co-occurred with transition to organic N cycling. However, ectomycorrhizal fungal decomposers correlated with small soil N and C stocks in forest, while root-associated ascomycetes associated with small N but large C stocks in heath, uncoupling C and N storage across vegetation types. We propose that contrasting, positive plant-microbial feedbacks stabilize vegetation trajectories, resulting in diverging soil C : N ratios at the landscape scale.", "doi": "10.1111/nph.18679", "pmid": "36519258", "labels": {"NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-10-10T08:52:43.763Z", "modified": "2024-01-16T13:48:33.308Z"}, {"entity": "publication", "iuid": "77aece2e31014f65adfcf55b29df6fa5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/77aece2e31014f65adfcf55b29df6fa5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/77aece2e31014f65adfcf55b29df6fa5"}}, "title": "Carbon substrate selects for different lineages of N2O reducing communities in soils under anoxic conditions", "authors": [{"family": "Maheshwari", "given": "Arpita", "initials": "A"}, {"family": "Jones", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-2723-6019", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c04ad1e78da45ee8b383fb09fc5d44a.json"}}, {"family": "Tiemann", "given": "Maren", "initials": "M"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}], "type": "journal-article", "published": "2023-02-00", "journal": {"title": "Soil Biology and Biochemistry", "issn": "0038-0717", "volume": "177", "pages": "108909", "issn-l": null}, "abstract": null, "doi": "10.1016/j.soilbio.2022.108909", "pmid": null, "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2022-12-19T16:49:11.444Z", "modified": "2024-01-16T13:48:34.049Z"}, {"entity": "publication", "iuid": "9582fbb5d0864897a3b6e0fd249a194b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9582fbb5d0864897a3b6e0fd249a194b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9582fbb5d0864897a3b6e0fd249a194b"}}, "title": "Unraveling negative biotic interactions determining soil microbial community assembly and functioning.", "authors": [{"family": "Romdhane", "given": "Sana", "initials": "S"}, {"family": "Spor", "given": "Aym\u00e9", "initials": "A", "orcid": "0000-0002-4707-9559", "researcher": {"href": "https://publications.scilifelab.se/researcher/38996366bf744d2e89398d9f5195c0c1.json"}}, {"family": "Aubert", "given": "Julie", "initials": "J", "orcid": "0000-0001-5203-5748", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ebb159d634b4e52bc684668009ce33c.json"}}, {"family": "Bru", "given": "David", "initials": "D"}, {"family": "Breuil", "given": "Marie-Christine", "initials": "MC"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}, {"family": "Mounier", "given": "Arnaud", "initials": "A"}, {"family": "Ouadah", "given": "Sarah", "initials": "S"}, {"family": "Tsiknia", "given": "Myrto", "initials": "M", "orcid": "0000-0002-0924-4509", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab7fd9f77f824b3196b57cc1d86d0636.json"}}, {"family": "Philippot", "given": "Laurent", "initials": "L", "orcid": "0000-0003-3461-4492", "researcher": {"href": "https://publications.scilifelab.se/researcher/45ef457126a748aebd40ff834d20085c.json"}}], "type": "journal article", "published": "2021-07-28", "journal": {"title": "ISME J", "issn": "1751-7370", "issn-l": "1751-7362"}, "abstract": "Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.", "doi": "10.1038/s41396-021-01076-9", "pmid": "34321619", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41396-021-01076-9"}], "notes": [], "created": "2021-10-01T09:03:46.208Z", "modified": "2021-12-06T13:48:07.440Z"}, {"entity": "publication", "iuid": "48ce3099225e4521962b6d5bc27cfb16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48ce3099225e4521962b6d5bc27cfb16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48ce3099225e4521962b6d5bc27cfb16"}}, "title": "Combined removal of organic micropollutants and ammonium in reactive barriers developed for managed aquifer recharge.", "authors": [{"family": "Modrzy\u0144ski", "given": "Jakub J", "initials": "JJ"}, {"family": "Aamand", "given": "Jens", "initials": "J"}, {"family": "Wittorf", "given": "Lea", "initials": "L", "orcid": "0000-0002-4478-7816", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f3a73ebc63c41fe8f487e5c0e6e12ad.json"}}, {"family": "Badawi", "given": "Nora", "initials": "N"}, {"family": "Hubalek", "given": "Valerie", "initials": "V"}, {"family": "Canelles", "given": "Arnau", "initials": "A"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}, {"family": "Albers", "given": "Christian N", "initials": "CN", "orcid": "0000-0001-7253-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/46a3cc1da4454d5bb6f4a595d31c05c9.json"}}], "type": "journal article", "published": "2021-02-15", "journal": {"title": "Water Res.", "issn": "1879-2448", "issn-l": "0043-1354", "volume": "190", "issue": null, "pages": "116669"}, "abstract": "Groundwater is an important drinking water resource. To ensure clean drinking water, managed aquifer recharge (MAR) could be an attractive solution when recharging with treated wastewater. The installation of reactive barriers, e.g. with compost or other organic materials at MAR facilities, may improve pollutant removal. To link pollutant transformation processes and microbiology in reactive barriers, we simulated infiltration through different sand-compost mixtures using laboratory columns with depth-specific sampling of water and barrier material. We also evaluated the effect of inoculation with activated sludge. Our focus was on the simultaneous removal of organic micropollutants and nitrogen species, with parallel monitoring of the development of microbial communities. During 17 weeks of operation, the columns were fed with synthetic wastewater containing five organic micropollutants (1-2 \u00b5g/L each) and ammonium (2 mg N/L). Unique communities developed in the columns in relation to barrier material, with high effects of compost addition and minor effect of inoculation. Removal of the micropollutant paracetamol (acetaminophen) occurred in all columns, while sulfamethoxazole was only removed in columns with 50% compost. By contrast, limited removal was observed for sulfadiazine, carbamazepine and diuron, with the latter two displaying transient removal, attributed sorption. Oxygen was depleted within the top few cm of the columns when compost was present, but this was sufficient to remove all ammonium through nitrification. The fate of accumulated nitrate at deeper layers depended on the fraction of compost, with more compost leading to removal of nitrate by denitrification, but also by dissimilatory nitrate reduction to ammonium, hampering the overall nitrogen removal efficiency. Introducing compost as reactive barrier in MAR facilities has a large effect on the microbial communities and processes, but whether it will provide overall cleaner water to the underlying aquifer is uncertain and will depend very much on the type of pollutant.", "doi": "10.1016/j.watres.2020.116669", "pmid": "33279750", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0043-1354(20)31204-5"}], "notes": [], "created": "2020-12-08T23:21:56.772Z", "modified": "2024-01-16T13:48:40.698Z"}]}